Well this is true to an extent. The developers do what you to play the game longer and always have something to do, but they don't want breeding to be your entire end-game experience. If you think this system is tiresome, you should have been around when you were given and egg and needed to bike around Kanto 4 times for it to hatch because it was step-based. There was also the flag system which made you spam battles so that your egg would learn its moves and abilities, which was also tiresome. With this breeding system however, you can pick up your egg then continue to do whatever you were doing; whether that was EV training, hunting for items, farming Pokemon, ect. In comparison to other breeding systems, I'd say that this one promotes actual gameplay more.
Believe it or not, you give up your Pokemon to keep the economy healthy. Let's start by taking a look at my Grumpig.
Here you see my 5x31 Bold Grumpig. In many aspects, this Pokemon is considered perfect and it cost me 800,000 yen to breed this. The breeding system averages IVs of the two parents, so what would happen if I were to create an exact replica of this Pokemon with the only difference being the gender? I could breed an infinite amount of perfect Grumpig without any cost. With that said, giving away your Pokemon is perhaps the most important aspect of this breeding system. Yes, PokeMMO developers and designers focus on the economy but that's what you have to do in an MMO environment. In the end, you will always get a more powerful Pokemon from breeding and that is the point.